I'm a huge proponent of using the right tool to do any job, whether the task is remodeling my kitchen cabinets, or processing timelapses.
In the case of timelapses, however, things get complicated as there are literally tens of different workflows that a photographer can use to create timelapse videos. How do you know which one is the right one, or which one is the best practice?

The answer to that question is one that my students hate to hear - and one that I hate to give - which is "it depends." Processing timelapses can be heavily taxing on your camera gear, your computer hardware, and your storage solutions. In developing a workflow, each TL shooter must look carefully at what computer power they have available to them, how much time they have available, and most importantly what their objectives / needs are.

No matter what post-processing workflow you choose to use to generate your timelapse clips and edit your showreels and finished movies, I will assume you are shooting in RAW and starting with either Canon CR2 or Nikon NEF files. If you're not, you should be.

It's also worth noting that I work on a PC that I bought from Dell. I can't afford a Mac with equivalent components. At the end of the day you can argue valid points about which one is better than the other, but you're using the same software so....I'm not convinced that there's a real difference. At any rate, here are the specs of my system, which cost about $1,700 to build:

Add sequence to render queue (if you want to generate an intermediate)

How here comes our first fork in the road. From AE, you can go in many different directions. You can save your sequences, and load them directly into Premiere through Dynamic Link Server, and use these in your editing timeline (but you have to pre-render).

Or, you can make intermediates. I chose this method because I like to have finished movie files for each clip available for viewing and archiving

Now comes the un-fun part of video. What type of intermediate file should you use? Again, the answer is "it depends." On what you might ask? You have to take into consideration things like storage space available, archive disk read/write speed, and color needs for your post-production environment. Here's what I do.

Intermediates - AVI Files / CineForm 4:4:4 Film Scan 2

The knowledgeable Tom Lowe of Timescapes fame recommended the CineForm codec in AVI container as an archival intermediate file format for his 4K timelapse work. According to Tom, the color fidelity was great, stood up to subsequent coloration work in DaVinci Resolve, and also AVI/Cineform Film Scan 2 also was editable in Premiere. Now, you have to understand that Tom is using a custom-built $20,000 monster PC (256 GB of RAM and dual nVidia GeForce 780 Titan cards!).

Nevertheless, on my meager machine I am able to render a 240 frame timelapse from CR2 files in this CineForm AVI compression format in about 10 minutes. File sizes are around 1.6 GB. I can't play these files back from my Drobo without dropping frames, but I can from my RAID-0 SSDs. Here's my workflow:

Add sequence to Render queue in AE

CineForm AVI format, FilmScan 2 quality 4:4:4 color

Drink coffee/beer

Place copy of files on SSD RAID drive array for editing

In Premiere, render previews to smooth editing.

That's it in a nutshell. Feel free to hit me with any questions via email or in the comments. As I said, there are many different ways to post-process timelapse. This is just the way I do it, and it works for me.